Hello Eric, I added *interactive_environment_plugins_directory = /home/galaxy/galaxy/config/plugins/interactive_environments* to *galaxy.ini*. Now I got the below error while clicking Rstudio and Ipython. Please find attached my config files and I was not sure how to change apache proxy config file:
Error Traceback: View as: Interactive http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# | Text http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# | XML http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# (full) http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# ⇝ AttributeError: 'Bunch' object has no attribute 'proxy_url' URL: http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626 Module weberror.evalexception.middleware:*364* in respond http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# view http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#
http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# app_iter *=* self*.*application*(*environ*,* detect_start_response*)* Module paste.recursive:*84* in __call__ http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# view http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#
http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# *return* self*.*application*(*environ*,* start_response*)* Module paste.httpexceptions:*633* in __call__ http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# view http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#
http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# *return* self*.*application*(*environ*,* start_response*)* Module galaxy.web.framework.base:*133* in __call__ http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# view http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#
http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# *return* self*.*handle_request*(* environ*,* start_response *)* Module galaxy.web.framework.base:*191* in handle_request http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# view http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#
http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# body *=* method*(* trans*,* ****kwargs *)* Module galaxy.web.framework.decorators:*68* in decorator http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# view http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#
http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# *return* func*(* self*,* trans*,* ***args*,* ****kwargs *)* Module galaxy.webapps.galaxy.controllers.visualization:*751* in render http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# view http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#
http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# self*.*_handle_plugin_error*(* trans*,* visualization_name*,* exception *)* Module galaxy.webapps.galaxy.controllers.visualization:*749* in render http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# view http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#
http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# *return* plugin*.*render*(* trans*=*trans*,* embedded*=*embedded*,* **** kwargs *)* Module galaxy.visualization.plugins.plugin:*138* in render http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# view http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#
http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# *return* self*.*_render*(* render_vars*,* trans*=*trans*,* embedded*=* embedded *)* Module galaxy.visualization.plugins.plugin:*284* in _render http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# view http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#
http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# *return* trans*.*fill_template*(* template_filename*,* template_lookup*=* self*.*template_lookup*,* ****render_vars *)* Module galaxy.web.framework.webapp:*811* in fill_template http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# view http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#
http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# *return* self*.*fill_template_mako*(* filename*,* ****kwargs *)* Module galaxy.web.framework.webapp:*825* in fill_template_mako http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# view http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#
http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# *return* template*.*render*(* ****data *)* Module mako.template:*296* in render http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# view http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#
http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# *return* runtime*.*_render*(*self*,* self*.*callable_*,* args*,* data*)* Module mako.runtime:*660* in _render http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# view http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#
http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# ****_kwargs_for_callable*(*callable_*,* data*)**)* Module mako.runtime:*692* in _render_context http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# view http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#
http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# _exec_template*(*inherit*,* lclcontext*,* args*=*args*,* kwargs*=*kwargs*)* Module mako.runtime:*718* in _exec_template http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# view http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#
http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# callable_*(*context*,* ***args*,* ****kwargs*)* Module rstudio_mako:*63* in render_body http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# view http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#
http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# notebook_pubkey_url *=* ie_request*.*url_template*(* '${PROXY_URL}/rstudio/auth-public-key'*)* Module galaxy.web.base.interactive_environments:*171* in url_template http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# view http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#
http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626# url *=* url_template*.*replace*(*'${PROXY_URL}'*,* str*(*self*.*attr*.* proxy_url*)**)* *AttributeError: 'Bunch' object has no attribute 'proxy_url'*
Thank you in advance.
Best wishes,
Mic
On Wed, Dec 23, 2015 at 4:14 AM, Eric Rasche esr@tamu.edu wrote:
Hi Mic,
Some comments/questions after looking over your conf:
- you've set "prefix" to /home/galaxy/galaxy, that prefix is used in
web proxying (not in finding paths to on-disk galaxy stuff), so unless you're running under a url prefix like http://fqdn/galaxy/ you may not want to set that (though I don't know if it will negatively affect you there. My gut says it won't cause an issue, but you never know)
- You'll need to set
interactive_environment_plugins_directory=/path/to/galaxy_root/config/plugins/interactive_environments
Let me know if that helps.
Cheers, Eric
On 12/22/2015 12:29 AM, Mic wrote:
Hello, I was trying more, but still no luck. Please find attached the new config files.
Thank you in advance.
Best wishes,
Mic
On Tue, Dec 22, 2015 at 11:26 AM, Mic mictadlo@gmail.com wrote:
Hi Eric, Thank you for your email. I have Galaxy installed in */home/galaxy/galaxy* and Apache Proxy is setup for *localhost:8080*. I modified the Apache config file further for GIE:
*RewriteEngine on RewriteRule ^/static/style/(.*) /home/galaxy/galaxy/static/june_2007_style/blue/$1 [L] RewriteRule ^/static/scripts/(.*) /home/galaxy/galaxy/static/scripts/packed/$1 [L] RewriteRule ^/static/(.*) /home/galaxy/galaxy/static/$1 [L] RewriteRule ^/favicon.ico /home/galaxy/galaxy/static/favicon.ico [L] RewriteRule ^/robots.txt /home/galaxy/galaxy/static/robots.txt [L] RewriteRule ^(.*) http://localhost:8080$1 [P] # IPython specific. Other IEs may require their own routes. ProxyPass /gie_proxy/ipython/api/kernels ws://localhost:8800/gie_proxy/ipython/api/kernels # Global GIE configuration ProxyPass /gie_proxy http://localhost:8800/gie_proxyhttp://localhost:8800/gie_proxy http://localhost:8800/gie_proxy ProxyPassReverse /gie_proxy http://localhost:8800/gie_proxyhttp://localhost:8800/gie_proxy http://localhost:8800/gie_proxy # Normal Galaxy configuration ProxyPass / http://localhost:8080 http://localhost:8080 ProxyPassReverse / http://localhost:8080 http://localhost:8080 * Did I modify the above files correctly?
*Thank you in advance, *
*Mic *
On Tue, Dec 22, 2015 at 4:15 AM, Eric Rasche < esr@tamu.eduesr@tamu.edu
wrote:
I'll look at this tonight, if no one else replies earlier today. Sorry to hear you're having these troubles Mic. GIEs can be tough to deploy. Thanks for bearing with us.
Cheers, Eric
2015-12-20 20:57 GMT-06:00 Mic < mictadlo@gmail.commictadlo@gmail.com> :
Hi all, I tried with *dynamic_proxy_manage=True* and *dynamic_proxy_manage=False*, but IE does not start inside Galaxy on a Annovar tab separated file (see attached).
I also tried the following commands, but without any luck:
$ node /home/galaxy/galaxy/lib/galaxy/web/proxy/js/lib/main.js --ip 0.0.0.0 --port 8800 --sessions /home/galaxy/galaxy/database/session_map.sqlite --cookie galaxysession --verbose Watching path /home/galaxy/galaxy/database/session_map.sqlite Listening on 0.0.0.0:8800
$ node /home/galaxy/galaxy/lib/galaxy/web/proxy/js/lib/main.js --ip 127.0.0.1 --port 8800 --sessions /home/galaxy/galaxy/database/session_map.sqlite --cookie galaxysession --verbose Watching path /home/galaxy/galaxy/database/session_map.sqlite Listening on 127.0.0.1:8800
$ node /home/galaxy/galaxy/lib/galaxy/web/proxy/js/lib/main.js --ip localhost --port 8800 --sessions /home/galaxy/galaxy/database/session_map.sqlite --cookie galaxysession --verbose Watching path /home/galaxy/galaxy/database/session_map.sqlite Listening on localhost:8800
My Galaxy is running on *0.0.0.0:8080 http://0.0.0.0:8080* view at * http://127.0.0.1:8080http://127.0.0.1:8080 http://127.0.0.1:8080*. I use Docker version 1.9.1, build a34a1d5.
Please find attached my *galaxy.ini* and apache proxy config file ( *000-default.conf*).
The following Apache modules I have enabled (*sudo a2enmod rewrite deflate expires proxy proxy_html xsendfile xml2enc proxy_wstunnel*)
What did I do wrong so I can not start Rstudio and IPython inside Galaxy?
Thank you in advance.
Mic
On Sat, Dec 19, 2015 at 1:12 PM, John Chilton < jmchilton@gmail.com jmchilton@gmail.com> wrote:
dynamic_proxy_manage_proxy=True is a terrible hack, I would set it to False and use supervisord if you have any inclination to at all. Like sqlite or the local job runner, it is just an attempt to make sure things work out of the box but it isn't that robust.
-John
On Sat, Dec 19, 2015 at 1:20 AM, Eric Rasche < esr@tamu.edu esr@tamu.edu> wrote:
- des. 2015 1.17 a.m. skrev "Mic" < mictadlo@gmail.com
mictadlo@gmail.com>:
> > Hi all, > Thank you for the responses. If I would use > "dynamic_proxy_manage_proxy=True" than Galaxy would execute
automatically:
> > /lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 \ > --port 8800 --sessions $GALAXY_ROOT/database/session_map.sqlite \ > --cookie galaxysession --verbose > > without the need to use supervisors config?
Yes. That's the idea. I'm not sure I trust it quite as much as
supervisord,
but it has worked quite well for us so far :-)
> > Thank you in advance. > > Mic > > > > On Sat, Dec 19, 2015 at 12:26 AM, Eric Rasche < esr@tamu.edu
esr@tamu.edu> wrote:
>> >> Hi Mic, >> >> Since you asked for the supervisord config... it would look
something
>> like this:] >> >> [program:galaxy_proxy] >> command=/usr/local/bin/node >> /path/to/galaxy/lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0
--port 8800
>> --sessions /path/to/galaxy/database/session_map.sqlite --cookie >> galaxysession --verbose >> numprocs=1 >> autostart=true >> autorestart=true >> startsecs=10 >> user=galaxy-user >> directory=/galaxy/home/directory >> umask=022 >> >> >> Galaxy can also automatically manage the proxy for you, if you set >> "dynamic_proxy_manage_proxy=True" in your galaxy.ini >> >> On 12/18/2015 01:23 AM, Björn Grüning wrote: >> > Hi, >> > >> > you need to have node installed. >> > >> > And then simply run: ./lib/galaxy/web/proxy/js/main.js --ip
0.0.0.0 \
>> > --port 8800 --sessions $GALAXY_ROOT/database/session_map.sqlite
\
>> > --cookie galaxysession --verbose >> > >> > from your Galaxy root dir. >> > >> > Cheers, >> > Bjoern >> > >> > Am 18.12.2015 um 06:58 schrieb Mic: >> >> Hello, >> >> I am using the latest stable Galaxy with PostgreSQL and Apache
Proxy.
>> >> I am >> >> trying to follow this instruction >> >> >> >>
http://galaxy.readthedocs.org/en/master/admin/interactive_environments.html http://galaxy.readthedocs.org/en/master/admin/interactive_environments.html
>> >> in order to be able to setup IE (Rstudio and Ipython).
However, I do
>> >> not >> >> know how to setup automatically Supervisord for this command: >> >> >> >> node $GALAXY_ROOT/lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 \ >> >> --port 8800 --sessions $GALAXY_ROOT/database/session_map.sqlite
\
>> >> --cookie galaxysession --verbose >> >> >> >> Thank you in advance >> >> >> >> Mic >> >> >> >> >> >> >> >> ___________________________________________________________ >> >> Please keep all replies on the list by using "reply all" >> >> in your mail client. To manage your subscriptions to this >> >> and other Galaxy lists, please use the interface at: >> >> https://lists.galaxyproject.org/
https://lists.galaxyproject.org/
>> >> >> >> To search Galaxy mailing lists use the unified search at: >> >> http://galaxyproject.org/search/mailinglists/
http://galaxyproject.org/search/mailinglists/
>> >> >> > ___________________________________________________________ >> > Please keep all replies on the list by using "reply all" >> > in your mail client. To manage your subscriptions to this >> > and other Galaxy lists, please use the interface at: >> > https://lists.galaxyproject.org/
https://lists.galaxyproject.org/
>> > >> > To search Galaxy mailing lists use the unified search at: >> > http://galaxyproject.org/search/mailinglists/
http://galaxyproject.org/search/mailinglists/
>> >> -- >> Eric Rasche >> Programmer II >> >> Center for Phage Technology >> Rm 312A, BioBio >> Texas A&M University >> College Station, TX 77843 >> 404-692-2048 >> esr@tamu.eduesr@tamu.edu >> >
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Eric Rasche Programmer II
Center for Phage Technology Rm 312A, BioBio Texas A&M University College Station, TX 77843 404-692-2048 esr@tamu.edu
-- Eric Rasche Programmer II
Center for Phage Technology Rm 312A, BioBio Texas A&M University College Station, TX 77843404-692-2048esr@tamu.edu